R Notebook

Check Enricher Results scRNAseq pipeline

library(Seurat)
library(tidyverse)
library(enrichR)

Welcome to enrichR
Checking connection ... 
Enrichr ... Connection is Live!
FlyEnrichr ... Connection is Live!
WormEnrichr ... Connection is Live!
YeastEnrichr ... Connection is Live!
FishEnrichr ... Connection is Live!
OxEnrichr ... Connection is Live!

Get the EnrichR libraries and run the function to check libraries and make plots

setEnrichrSite("Enrichr") # Human genes

Connection changed to https://maayanlab.cloud/Enrichr/
Connection is Live!

# list of all the databases
# get the possible libraries
dbs <- listEnrichrDbs()

# this will list the possible libraries
dbs

# select libraries with cell types
db <- c('CellMarker_Augmented_2021','Azimuth_Cell_Types_2021')

# function for a quick look
checkCelltypes <- function(cluster_num = 0){
  clusterX <- ClusterMarkers %>% filter(cluster == cluster_num & avg_log2FC > 0.25)
  genes <- clusterX$gene
  # the cell type libraries
  # get the results for each library
  clusterX.cell <- enrichr(genes, databases = db)
  # visualize the results
print(plotEnrich(clusterX.cell[[1]], showTerms = 20, numChar = 40, y = "Count", orderBy = "P.value", title = 'CellMarker_Augmented_2021'))
print(plotEnrich(clusterX.cell[[2]], showTerms = 20, numChar = 40, y = "Count", orderBy = "P.value", title = 'Azimuth_Cell_Types_2021'))

}

Read in the data from HPCs

ClusterMarkers <- read.csv("/Users/rhalenathomas/Documents/Data/scRNAseq/ADHD_ZNZ_Mcgill/ADHDresultsFeb10/NSC/step7/info7/marker/ClusterMarkers.csv")
  
  

Run to get markers for each cluster

cluster0 <- checkCelltypes(cluster_num = 0)

Uploading data to Enrichr... Done.
  Querying CellMarker_Augmented_2021... Done.
  Querying Azimuth_Cell_Types_2021... Done.
Parsing results... Done.

Cluster 0 gabaergic neurons

cluster1 <- checkCelltypes(cluster_num = 1)

Uploading data to Enrichr... Done.
  Querying CellMarker_Augmented_2021... Done.
  Querying Azimuth_Cell_Types_2021... Done.
Parsing results... Done.

Cluster 1 fibroblast

cluster2 <- checkCelltypes(cluster_num = 2)

Uploading data to Enrichr... Done.
  Querying CellMarker_Augmented_2021... Done.
  Querying Azimuth_Cell_Types_2021... Done.
Parsing results... Done.

Cluster 2 is neurons

# cluster 3
cluster3 <- checkCelltypes(cluster_num = 3)

Uploading data to Enrichr... Done.
  Querying CellMarker_Augmented_2021... Done.
  Querying Azimuth_Cell_Types_2021... Done.
Parsing results... Done.

Cluster 3 are proliferating progenitors

# cluster 4
cluster4 <- checkCelltypes(cluster_num = 4)

Uploading data to Enrichr... Done.
  Querying CellMarker_Augmented_2021... Done.
  Querying Azimuth_Cell_Types_2021... Done.
Parsing results... Done.

Cluster 4 - neural stem, proliferating

# cluster 5
cluster5 <- checkCelltypes(cluster_num = 5)

Uploading data to Enrichr... Done.
  Querying CellMarker_Augmented_2021... Done.
  Querying Azimuth_Cell_Types_2021... Done.
Parsing results... Done.

Cluster 5 proliferating neural stem cells

# cluster 6
cluster6 <- checkCelltypes(cluster_num = 6)

Uploading data to Enrichr... Done.
  Querying CellMarker_Augmented_2021... Done.
  Querying Azimuth_Cell_Types_2021... Done.
Parsing results... Done.

Cluster 6 embryonic coritical astrocytes, neurons

# cluster 7
cluster7 <- checkCelltypes(cluster_num = 7)

Uploading data to Enrichr... Done.
  Querying CellMarker_Augmented_2021... Done.
  Querying Azimuth_Cell_Types_2021... Done.
Parsing results... Done.

Cluster 7 - dividing cells, neural stem cells

# cluster 8
cluster8 <- checkCelltypes(cluster_num = 8)

Uploading data to Enrichr... Done.
  Querying CellMarker_Augmented_2021... Done.
  Querying Azimuth_Cell_Types_2021... Done.
Parsing results... Done.

Cluster 8 - muscle??

# cluster 9
cluster9 <- checkCelltypes(cluster_num = 9)

Uploading data to Enrichr... Done.
  Querying CellMarker_Augmented_2021... Done.
  Querying Azimuth_Cell_Types_2021... Done.
Parsing results... Done.

Cluster 9 - cholinergic neurons, OPC

# cluster 10
cluster10 <- checkCelltypes(cluster_num = 10)

Uploading data to Enrichr... Done.
  Querying CellMarker_Augmented_2021... Done.
  Querying Azimuth_Cell_Types_2021... Done.
Parsing results... Done.

T cell, vasculature, NSC

# cluster 11
cluster11 <- checkCelltypes(cluster_num = 11)

Uploading data to Enrichr... Done.
  Querying CellMarker_Augmented_2021... Done.
  Querying Azimuth_Cell_Types_2021... Done.
Parsing results... Done.

NPC - prefrontal cortex